Hopefully we'll be able to get a better explanation as we get more chances to see the movie or written transcripts, but I think I have a theory explaining why Dr. Ana Stelline was in a bubble. While it is a bit lengthy, I believe it does tie together all the salient points.
I fail to understand how the side that has her in a bubble, making
memories, is moving forward with their (the replicants') plan?
We know that Deckard and the underground replicants wanted to protect Stelline knowing that, in hiding, as they knew they would be hunted relentlessly. Deckard's part was that he was able to "scramble the records", fabricating evidence that twins were born, a boy and a girl.
When K is examining the DNA, he identifies a genetic anomaly that results in a compromised immune system--a story separately verified by Stelline, saying she was unable leave the planet and could only safely live in the bubble. The other way to look at this, however, is the genetic anomaly was a deliberate ruse to prevent her emigration off-world. That is, ensuring that no matter what happened to her in the orphanage or beyond, she would be marooned on earth.
Considering the squalor she endured in the scrap yard orphanage in San Diego, it is highly unlikely this immuno-compromised condition is real. And even if a bit of a stretch, this could also have a happy by-product keeping her insulated from physical danger.
She's now 30 years of age and they are no closer to finding out how
to have children of their own. Are they just having sex with each
other for 30 years hoping to hit the jackpot again?
The events of Blade Runner: Black Out 2022 chronicle how Replicants came to be prohibited after their assault on the world with an EMP. It is another ten years before the Wallace Corp is permitted to start up new production on Replicants. That means for Stelline's first 10 years of living, the zeitgeist of the world was heavily anti-replicant; not an environment that would be accepting of the notion that replicants are more human than they were given credit for.
So around 2032 marks the beginning of new Replicants (Nexus 8's under Wallace Corp), in which the underground Replicants are still unlikely to provide a real, physical (and existential) threat. There's a single producer again and they are ridiculously obedient. But as we've seen from the original BR as well as BR2049, believable memories seem to be the root causes of all the chaos. This would explain why (for the viewers' benefit) Stelline tells K that implanting real memories into replicants is illegal.
- Rachel--and her memories of Tyrell's niece (believed to be her own)--drives her to confront Deckard in his home and then run away.
- K (or Joe) believing to be the boy with the horse lies to Joshi about retiring the Replicant child.
I mean they lead us to believe she's more important than that, yet, they're not using her in any way to figure it out.
So ultimately, I believe the underground resistance was just biding their time waiting for the best opportunity to show the world that they are as human as humans, and that they would be prepared and ready to fight/defend Stelline as their figurehead when she gets outed as a Replicant offspring. In the meantime, all time "lost" in the interim just had the bonus of more Replicants being indoctrinated with Stelline's fabricated/authentic memories--presumably, this would be beneficial to the resistance in that they might be more sympathetic to the resistance's cause, as K was.
That the first Replicant offspring also happened to inadvertently become the world's foremost memory creator for Wallace Corp. seems to be the only enormous plot leap.